2-133574525-C-T

Variant names:

• chr2-133574525-C-T
• rs891821
• XM_005263660.5:c.-61-56938G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_005263660.5(NCKAP5):​c.-61-56938G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,352 control chromosomes in the GnomAD database, including 19,244 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (19244 hom., cov: 30)
• Consequence: NCKAP5 XM_005263660.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890
• Publications: 3 publications found

Genes affected

NCKAP5 (HGNC:29847): (NCK associated protein 5) Predicted to be involved in microtubule bundle formation and microtubule depolymerization. Predicted to be active in microtubule plus-end. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCKAP5	XM_005263660.5	c.-61-56938G>A		intron_variant	Intron 1 of 17		XP_005263717.1
NCKAP5	XM_011511099.4	c.-129-15408G>A		intron_variant	Intron 1 of 18		XP_011509401.1
NCKAP5	XM_011511100.4	c.-129-15408G>A		intron_variant	Intron 1 of 18		XP_011509402.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74630 AN: 151238 Hom.: 19230 Cov.: 30

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.450

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.493 AC: 74682 AN: 151352 Hom.: 19244 Cov.: 30 AF XY: 0.499 AC XY: 36864 AN XY: 73868

African (AFR) AF: 0.355 AC: 14610 AN: 41168

American (AMR) AF: 0.453 AC: 6894 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1650 AN: 3472

East Asian (EAS) AF: 0.471 AC: 2407 AN: 5114

South Asian (SAS) AF: 0.579 AC: 2779 AN: 4796

European-Finnish (FIN) AF: 0.651 AC: 6745 AN: 10368

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38079 AN: 67904

Other (OTH) AF: 0.452 AC: 951 AN: 2102

Alfa AF: 0.524 Hom.: 60152

Bravo AF: 0.467

Asia WGS AF: 0.542 AC: 1881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.7
DANN	Benign	0.58
PhyloP100		-0.089

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs891821; hg19: chr2-134332096;